Thank you Jason,
I’ll try what you suggested. I have one question.
The installation of Python 2.7 via MacPorts will place it in /opt/local/bin.
Should I remove then the native MacOS installations in /usr/bin (i.e. python2.6, python2.7)?
Wouldn’t there be conflicts having python installed in two different directories?
And a trivial one just to satisfy my curiosity.
How come that I did not encounter this problem in the amber parallel installation on the Mac Pro?
Regards
George
> On 16 May 2015, at 02:47, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Fri, May 15, 2015 at 4:22 PM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>
>> I’ve successfully installed mmpbsa.py.MPI on the Mac Pro following the
>> instructions given in:
>>
>> http://jswails.wikidot.com/installing-amber12-and-ambertools-13.
>>
>> I followed the same installation procedure on a PowerBook Pro (OS X
>> v.10.10.3). Prior to the installation, I deleted the /opt directory and
>> re-installed it.
>>
>> I selected the proper compilers (see below)
>>
>> Selecting 'mp-gcc48' for 'gcc' succeeded. 'mp-gcc48' is now active.
>>
>> Selecting 'mpich-gcc48-fortran' for 'mpi' succeeded. 'mpich-gcc48-fortran'
>> is now active.
>>
>>
>> Completing the parallel installation of amber through out no error
>> messages. However, mmpbsa.py.MPI was NOT installed.
>>
>> mpi4py_install.log indicates that file _configtest.o was built for the
>> wrong architecture (i386) and not for x86_64.
>>
>> Anything that can be done to save the day? Thanks in advance for any
>> suggestions
>>
>> George
>>
>> The complete .log file is below.
>>
>> unning build
>> running build_py
>> creating build
>> creating build/lib.macosx-10.10-intel-2.7
>> creating build/lib.macosx-10.10-intel-2.7/mpi4py
>> copying src/__init__.py -> build/lib.macosx-10.10-intel-2.7/mpi4py
>> copying src/rc.py -> build/lib.macosx-10.10-intel-2.7/mpi4py
>> creating build/lib.macosx-10.10-intel-2.7/mpi4py/include
>> creating build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.h ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.MPI.h ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.MPI_api.h ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/__init__.pxd ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/MPI.pxd ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi_c.pxd ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/__init__.pyx ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi.pxi ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> copying src/include/mpi4py/mpi4py.i ->
>> build/lib.macosx-10.10-intel-2.7/mpi4py/include/mpi4py
>> running build_ext
>> MPI C compiler: /opt/local/bin/mpicc
>> MPI C++ compiler: /opt/local/bin/mpicxx
>> MPI linker: /opt/local/bin/mpicc
>> checking for MPI compile and link ...
>> /opt/local/bin/mpicc -arch x86_64 -arch i386 -pipe -fno-strict-aliasing
>> -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes
>> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
>> -c _configtest.c -o _configtest.o
>>
>
> Look right here ^^^
>
> You see "-arch x86_64 -arch i386" in the compilation line. Based on your
> error message below, I suspect what this means is the "-arch" flag in the
> host compiler is either ignored or it overwrites (so that -arch i386
> overrides -arch x86_64), rather than specifying two target architectures.
>
> It's not entirely straightforward to change these flags, either. Python's
> distutils uses the same CFLAGS and compiler as those used to compile Python
> originally, and Apple builds their Python binary for both architectures.
> mpi4py, though, needs mpicc, which in this case does *not* wrap the host
> compiler (/usr/bin/clang) but rather /opt/local/bin/gcc instead (you can
> use "mpicc -show" to verify this).
>
> Long story short: you will not have much luck building this mpi4py using
> the system Python. I recommend using MacPorts to install Python 2.7, and
> since you're using MacPorts to install your MPI also, go ahead and have
> MacPorts install mpi4py as well (that way Amber won't try to).
>
> So something like this:
>
> sudo port install python27 py27-tkinter py27-mpi4py py27-matplotlib
> py27-scipy py27-pandas
>
> That should give you the basic Python infrastructure with the most common
> Python libraries and everything that every program in Amber depends on
> (like mdout_analyzer.py, MMPBSA.py, parmed.py, xparmed.py, and by extension
> ante-MMPBSA.py). After you do this, make sure to reconfigure so that Amber
> knows to switch its default Python interpreter.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat May 16 2015 - 06:30:02 PDT
